Summary of Study ST001917

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001208. The data can be accessed directly via it's Project DOI: 10.21228/M8JX2X This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

Study ID	ST001917
Study Title	Myocardial Rev-erb-mediated diurnal metabolic rhythm (Part 3/3)
Study Summary	The snap-frozen mouse heart ventricles that was harvested at ZT6 or ZT18 from both WT and Rev-erb cardiomyocytes specific KO mice were used for metabolomics study.
Institute	Baylor College of Medicine
Last Name	Song
First Name	Shiyang
Address	One Baylor Plaza
Email	shiyangs@bcm.edu
Phone	7137983159
Submit Date	2021-09-10
Raw Data Available	Yes
Analysis Type Detail	LC-MS
Release Date	2022-12-24
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001208
Project DOI:	doi: 10.21228/M8JX2X
Project Title:	Myocardial Rev-erb-mediated diurnal metabolic rhythm
Project Summary:	Agonists and antagonists of nuclear receptor Rev-erbα/β, key components of the circadian clock, can benefit the heart. Here, we show that mice with cardiomyocyte-specific knockout (KO) of Rev-erbα/β display progressive cardiac dilation and lethal heart failure. Inducible ablation of Rev-erbα/β in adult hearts causes similar phenotypes. Impaired fatty acid oxidation in the KO myocardium, particularly in the light cycle, precedes contractile dysfunctions with a reciprocal overreliance on carbohydrate utilization, particularly in the dark cycle. These findings delineate temporal coordination between clock-mediated anticipation and nutrient-induced response in myocardial metabolism.
Institute:	Baylor College of Medicine
Last Name:	Song
First Name:	Shiyang
Address:	One Baylor Plaza, Houston, Texas, 77030, USA
Email:	shiyangs@bcm.edu
Phone:	7137983159

Subject:

Subject ID:	SU001995
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090
Age Or Age Range:	10 weeks
Gender:	Male

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id	local_sample_id	Group	Genotype	Experimental variables
SA177727	KO_ZT18_2	KO_ZT18	Rev-erb cardiomyocyte specific knock out	KO mouse heart ventrcle harvest at ZT18
SA177728	KO_ZT18_1	KO_ZT18	Rev-erb cardiomyocyte specific knock out	KO mouse heart ventrcle harvest at ZT18
SA177729	KO_ZT18_3	KO_ZT18	Rev-erb cardiomyocyte specific knock out	KO mouse heart ventrcle harvest at ZT18
SA177730	KO_ZT6_3	KO_ZT6	Rev-erb cardiomyocyte specific knock out	KO mouse heart ventrcle harvest at ZT6
SA177731	KO_ZT6_1	KO_ZT6	Rev-erb cardiomyocyte specific knock out	KO mouse heart ventrcle harvest at ZT6
SA177732	KO_ZT6_2	KO_ZT6	Rev-erb cardiomyocyte specific knock out	KO mouse heart ventrcle harvest at ZT6
SA177733	WT_ZT18_3	WT_ZT18	wild type control	WT mouse heart ventrcle harvest at ZT18
SA177734	WT_ZT18_1	WT_ZT18	wild type control	WT mouse heart ventrcle harvest at ZT18
SA177735	WT_ZT18_2	WT_ZT18	wild type control	WT mouse heart ventrcle harvest at ZT18
SA177736	WT_ZT6_2	WT_ZT6	wild type control	WT mouse heart ventrcle harvest at ZT6
SA177737	WT_ZT6_1	WT_ZT6	wild type control	WT mouse heart ventrcle harvest at ZT6
SA177738	WT_ZT6_3	WT_ZT6	wild type control	WT mouse heart ventrcle harvest at ZT6

Showing results 1 to 12 of 12

Showing results 1 to 12 of 12

Collection:

Collection ID:	CO001988
Collection Summary:	Snap-frozen heart ventricles were collected from both WT and Rev-erb cardiomyocyte-specific KO mice at ZT6 or ZT18
Sample Type:	Heart

Treatment:

Treatment ID:	TR002007
Treatment Summary:	No special treatment

Sample Preparation:

Sampleprep ID:	SP002001
Sampleprep Summary:	Heart ventricle tissues were harvested from male mice at 2.5 months of age (n = 3 at each condition) and snap-frozen in liquid nitrogen. Data were acquired in multiple reaction monitoring (MRM) using Agilent QQQ LC-MS systems. Separation of TCA and glycolysis metabolites were performed using 5 mM ammonium acetate in water as buffer pH 9.9 (A), and 100% acetonitrile as buffer (B) using Luna 3 µM NH2 column (Phenomenex, Torrance, CA) and measured 6495 triple quadrupole mass spectrometer via ESI negative mode (Agilent Technologies, Santa Clara, CA). The Gradient used is as follows: 0-20 min-80% B (Flow rate 0.2ml/min); 20-20.10 min- 80% to 2 % B; 20.10-25 min-2% B (Flow rate 0.3ml/min); 25-30 min 80% B (Flowrate 0.35ml/min); 30-35 min-80%B (Flow rate 0.4ml/min); 35-38 min 80% B (Flow rate 0.4ml/min); followed by re-equilibration at the end of the gradient to the initial starting condition 80% B at Flow rate of 0.2 ml/min. Separation and measurement of amino acids were performed using Zorbax eclipse XDB C-18, 1.8 micron, 4.6 x 100 mm column on 6495 triple quadrupole mass spectrometer via ESI Positive mode (Agilent Technologies, Santa Clara, CA). Mobile phases A and B were 0.1% formic acid in water and acetonitrile, respectively. The gradient used is as follows: 0 min-2% B; 6 min- 2% of B, 6.5 min-30 % B, 7 min- 90% of B, 12 min 95% of B, 13 min 2% of B followed by re-equilibration at the end of the gradient 20 min to the initial starting condition 2% of B. Flow rate: 0.2 ml/min. Separation and measurement of CoA's and carnitines were performed using Zorbax eclipse XDB C-18, 1.8 micron, 4.6 x 100 mm column on 6495 triple quadrupole mass spectrometer via ESI Positive mode (Agilent Technologies, Santa Clara, CA). Mobile phases A and B were 0.1% formic acid in water and acetonitrile, respectively. Gradient used is as follows: 0 min-2% B; 6 min- 2% of B, 6.5 min-30 % B, 7 min- 90% of B, 12 min 95% of B,13 min 2% of B followed by re-equilibration at end of the gradient 20 min to the initial starting condition 2% of B. Flow rate: 0.2 ml/min. Separation and measurement of nucleotides were performed using Zorbax eclipse XDB C-18, 1.8 micron, 4.6 x 100 mm column on 6495 triple quadrupole mass spectrometer via ESI Positive mode (Agilent Technologies, Santa Clara, CA). Mobile phases A and B were 0.1% formic acid in water and acetonitrile, respectively. The gradient used is as follows: 0-6 min 2% B, 6-6.50 min 30% B, 7-12 min 95% B, 12-13 min 2% B, and re-equilibration till the end of the gradient 20 min. Flow rate: 0.2 ml/min). The data were normalized with internal standards, and log2 transformed on a per-sample, per-method basis. Statistical analyses were performed with either ANOVA or t-test in R Studio (R Studio Inc., Boston, MA). Differential metabolites were identified by adjusting the p-values for multiple testing at an FDR (Benjamini Hochberg method) threshold of <0.25.

Sampleprep ID:

SP002001

Sampleprep Summary:

Heart ventricle tissues were harvested from male mice at 2.5 months of age (n = 3 at each condition) and snap-frozen in liquid nitrogen. Data were acquired in multiple reaction monitoring (MRM) using Agilent QQQ LC-MS systems. Separation of TCA and glycolysis metabolites were performed using 5 mM ammonium acetate in water as buffer pH 9.9 (A), and 100% acetonitrile as buffer (B) using Luna 3 µM NH2 column (Phenomenex, Torrance, CA) and measured 6495 triple quadrupole mass spectrometer via ESI negative mode (Agilent Technologies, Santa Clara, CA). The Gradient used is as follows: 0-20 min-80% B (Flow rate 0.2ml/min); 20-20.10 min- 80% to 2 % B; 20.10-25 min-2% B (Flow rate 0.3ml/min); 25-30 min 80% B (Flowrate 0.35ml/min); 30-35 min-80%B (Flow rate 0.4ml/min); 35-38 min 80% B (Flow rate 0.4ml/min); followed by re-equilibration at the end of the gradient to the initial starting condition 80% B at Flow rate of 0.2 ml/min. Separation and measurement of amino acids were performed using Zorbax eclipse XDB C-18, 1.8 micron, 4.6 x 100 mm column on 6495 triple quadrupole mass spectrometer via ESI Positive mode (Agilent Technologies, Santa Clara, CA). Mobile phases A and B were 0.1% formic acid in water and acetonitrile, respectively. The gradient used is as follows: 0 min-2% B; 6 min- 2% of B, 6.5 min-30 % B, 7 min- 90% of B, 12 min 95% of B, 13 min 2% of B followed by re-equilibration at the end of the gradient 20 min to the initial starting condition 2% of B. Flow rate: 0.2 ml/min. Separation and measurement of CoA's and carnitines were performed using Zorbax eclipse XDB C-18, 1.8 micron, 4.6 x 100 mm column on 6495 triple quadrupole mass spectrometer via ESI Positive mode (Agilent Technologies, Santa Clara, CA). Mobile phases A and B were 0.1% formic acid in water and acetonitrile, respectively. Gradient used is as follows: 0 min-2% B; 6 min- 2% of B, 6.5 min-30 % B, 7 min- 90% of B, 12 min 95% of B,13 min 2% of B followed by re-equilibration at end of the gradient 20 min to the initial starting condition 2% of B. Flow rate: 0.2 ml/min. Separation and measurement of nucleotides were performed using Zorbax eclipse XDB C-18, 1.8 micron, 4.6 x 100 mm column on 6495 triple quadrupole mass spectrometer via ESI Positive mode (Agilent Technologies, Santa Clara, CA). Mobile phases A and B were 0.1% formic acid in water and acetonitrile, respectively. The gradient used is as follows: 0-6 min 2% B, 6-6.50 min 30% B, 7-12 min 95% B, 12-13 min 2% B, and re-equilibration till the end of the gradient 20 min. Flow rate: 0.2 ml/min). The data were normalized with internal standards, and log2 transformed on a per-sample, per-method basis. Statistical analyses were performed with either ANOVA or t-test in R Studio (R Studio Inc., Boston, MA). Differential metabolites were identified by adjusting the p-values for multiple testing at an FDR (Benjamini Hochberg method) threshold of <0.25.

Combined analysis:

Analysis ID	AN003115
Analysis type	MS
Chromatography type	GC
Chromatography system	Agilent 1290
Column	Agilent Zorbax Eclipse Plus C18 (100 x 2.1mm, 1.8 um)
MS Type	ESI
MS instrument type	Triple quadrupole
MS instrument name	Agilent 6490 QQQ
Ion Mode	POSITIVE
Units	pmoles/l

Chromatography:

Chromatography ID:	CH002300
Chromatography Summary:	Separation of TCA and glycolysis metabolites were performed using 5 mM ammonium acetate in water as buffer pH 9.9 (A), and 100% acetonitrile as buffer (B) using Luna 3 µM NH2 column (Phenomenex, Torrance, CA) and measured 6495 triple quadrupole mass spectrometer via ESI negative mode (Agilent Technologies, Santa Clara, CA). The Gradient used is as follows: 0-20 min-80% B (Flow rate 0.2ml/min); 20-20.10 min- 80% to 2 % B; 20.10-25 min-2% B (Flow rate 0.3ml/min); 25-30 min 80% B (Flowrate 0.35ml/min); 30-35 min-80%B (Flow rate 0.4ml/min); 35-38 min 80% B (Flow rate 0.4ml/min); followed by re-equilibration at the end of the gradient to the initial starting condition 80% B at Flow rate of 0.2 ml/min. Separation and measurement of amino acids were performed using Zorbax eclipse XDB C-18, 1.8 micron, 4.6 x 100 mm column on 6495 triple quadrupole mass spectrometer via ESI Positive mode (Agilent Technologies, Santa Clara, CA). Mobile phases A and B were 0.1% formic acid in water and acetonitrile, respectively. The gradient used is as follows: 0 min-2% B; 6 min- 2% of B, 6.5 min-30 % B, 7 min- 90% of B, 12 min 95% of B, 13 min 2% of B followed by re-equilibration at the end of the gradient 20 min to the initial starting condition 2% of B. Flow rate: 0.2 ml/min. Separation and measurement of CoA's and carnitines were performed using Zorbax eclipse XDB C-18, 1.8 micron, 4.6 x 100 mm column on 6495 triple quadrupole mass spectrometer via ESI Positive mode (Agilent Technologies, Santa Clara, CA). Mobile phases A and B were 0.1% formic acid in water and acetonitrile, respectively. Gradient used is as follows: 0 min-2% B; 6 min- 2% of B, 6.5 min-30 % B, 7 min- 90% of B, 12 min 95% of B,13 min 2% of B followed by re-equilibration at end of the gradient 20 min to the initial starting condition 2% of B. Flow rate: 0.2 ml/min. Separation and measurement of nucleotides were performed using Zorbax eclipse XDB C-18, 1.8 micron, 4.6 x 100 mm column on 6495 triple quadrupole mass spectrometer via ESI Positive mode (Agilent Technologies, Santa Clara, CA). Mobile phases A and B were 0.1% formic acid in water and acetonitrile, respectively. The gradient used is as follows: 0-6 min 2% B, 6-6.50 min 30% B, 7-12 min 95% B, 12-13 min 2% B, and re-equilibration till the end of the gradient 20 min. Flow rate: 0.2 ml/min).
Instrument Name:	Agilent 1290
Column Name:	Agilent Zorbax Eclipse Plus C18 (100 x 2.1mm, 1.8 um)
Chromatography Type:	GC

MS:

MS ID:	MS002896
Analysis ID:	AN003115
Instrument Name:	Agilent 6490 QQQ
Instrument Type:	Triple quadrupole
MS Type:	ESI
MS Comments:	The data were normalized with internal standards, and log2 transformed on a per-sample, per-method basis. Statistical analyses were performed with either ANOVA or t-test in R Studio (R Studio Inc., Boston, MA). Differential metabolites were identified by adjusting the p-values for multiple testing at an FDR (Benjamini Hochberg method) threshold of <0.25.
Ion Mode:	POSITIVE